Generative AI Guided Design of High-Affinity T cell Receptors

Abstract

Developing T cell receptors (TCRs) with sufficiently high affinity for tumor antigens (TAs) remains a fundamental challenge in TCR-T immunotherapy. Experimental methods such as affinity maturation and high-throughput screening have enabled the identification of TCRs with enhanced activity. However, their efficiency is often constrained by limited throughput, insufficient coverage, and the generally lower affinities of naturally occurring TCRs toward TAs. To address these challenges, we present TCRPPO2, an integrated AI-driven, in silico affinity maturation framework for peptide-specific TCR optimization. Using reinforcement learning, TCRPPO2 learns mutation policies that iteratively enhance the TCR binding affinity to the target peptide, derived from predictive models trained on carefully curated interaction data. The model is further augmented by a generative AI critic model that discourages implausible designs to ensure the biophysical validity. The designs are further screened by robust post-screening methods that leverage diverse functional annotations and physical prior knowledge. We applied TCRPPO2 to the clinically relevant MART-1 antigen and experimentally validated the designed candidates in Jurkat cell-based functional assays. Among the five engineered TCRs, all of which demonstrated positive cellular responses, three showed significantly increased activities relative to their templates and one showed substantial enhancement. These functional gains were consistent with more favorable interaction energy from structural and physical modeling. Together, our results support a generalizable paradigm for TCR engineering, in which learned mutation policies can efficiently navigate the peptide-specific binding landscape of TCRs and propose biologically enhanced candidates without explicit structural supervision, offering a practical route for early-stage computational TCR optimization for challenging tumor antigens.